# Mitochondrial Cyt b Reveals Low Diversity and Basin-Scale Population Structure in Black Carp (Mylopharyngodon piceus) from the Yangtze, Pearl and Red River Basins

## TL;DR

Black carp populations in East Asia show low genetic diversity and distinct regional structures, suggesting the need for targeted conservation strategies to protect their genetic variation.

## Contribution

The study reveals basin-scale population structure and low mitochondrial diversity in black carp, providing a baseline for conservation before recent management changes.

## Key findings

- Low mitochondrial genetic diversity was observed, particularly in Pearl and Red River populations.
- Yangtze populations showed higher diversity but were distinct from Pearl–Red River groups.
- A single dominant haplotype was shared across all populations, indicating recent demographic expansion.

## Abstract

Black carp is a large freshwater fish native to East Asia that feeds mainly on snails and clams, helping to control pests and maintain river ecosystems. However, wild stocks have declined because of overfishing, river regulation, pollution and poorly regulated stocking practices. Here, we analysed a mitochondrial DNA marker (cytochrome b, Cyt b) in fish sampled at seven sites in the Yangtze, Pearl and Red River basins during 2008–2009. These pre-ban samples provide a snapshot of maternal lineages before the ten-year fishing ban in key reaches of the Yangtze River and before recent adjustments to stocking practices. We found generally low mitochondrial genetic diversity, especially in the Pearl and Red River groups, which may limit the capacity of local populations to cope with environmental change and disease. Yangtze populations werve more diverse but already differed between the middle–lower Yangtze and an upstream site and showed broad separation from the combined Pearl–Red River group. These patterns suggest that uncritical movements of broodstock or juveniles among basins could erode remaining genetic differences. Protecting key habitats, using genetically diverse, locally adapted broodstock and avoiding unnecessary mixing among basins will help conserve black carp and support more sustainable river fisheries.

The black carp (Mylopharyngodon piceus) is an ecologically and economically important freshwater fish native to China and neighbouring regions, but its wild stocks have declined sharply in recent decades. We analysed mitochondrial cytochrome b (Cyt b) sequences from 100 individuals collected in 2008–2009 from four Yangtze River, two Pearl River and one Red River populations to assess genetic diversity and structure as a pre-ban baseline for maternal lineages. Sixteen polymorphic sites defined 17 haplotypes, with a single dominant haplotype (Hap2) shared across all populations. Haplotype diversity was high but nucleotide diversity low, and neutrality tests together with mismatch-distribution analyses were consistent with a recent Late Pleistocene demographic expansion. Pairwise FST values ranged from negligible differentiation among middle–lower Yangtze populations to pronounced differentiation between the upstream Yangtze population (SS) and middle–lower populations and between the Yangtze and the combined Pearl–Red basins, whereas Pearl and Red River populations showed no significant divergence and high mitochondrial homogeneity, consistent with substantial historical connectivity. Overall, the Cyt b data indicate low mitochondrial diversity and shallow but significant inter-basin structuring, providing preliminary mtDNA-based evidence that Yangtze and Pearl–Red populations represent candidate conservation and management units, and highlighting the need for nuclear genomic markers and contemporary sampling to refine drainage-scale units and evaluate recent management effects.